library(tidyverse)
source("MAP_functions.R")
Subject 26
SNP_analysis_pipeline(subject_id = 26)
[1] "SUBJECT_ID is 26"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 24514"
[1] "Num bases in R recomb = blocks 24514"
[1] "Num bases in V recomb = blocks 3567"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036306"
[1] "Numbers of C bases above cutoff is 1036204"
[1] "Numbers of V bases above cutoff is 1035660"
[1] "Number of iSNP positions = 5311"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 36"
[1] "R only rare iSNPs (RonlyRIrare) = 16"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 6"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5229"
[1] "All rare fixed SNPs (AllFrare) = 1179"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 12"
[1] "All iSNPs (AllRI) = 16"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 1"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 1"
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 18 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 334"
[1] "Number cDenovo Non-Ref SNPs for C = 1528"
[1] "Number cDenovo iSNPs for C = 1"
[1] "Number cDenovo Ref SNPs for R = 336"
[1] "Number cDenovo Non-Ref SNPs for R = 1526"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 335"
[1] "Number cDenovo Non-Ref SNPs for V = 1531"
[1] "Number cDenovo iSNPs for V = 1"
[[1]]
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Subject 32
SNP_analysis_pipeline(subject_id = 32)
[1] "SUBJECT_ID is 32"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 1680"
[1] "Num bases in R recomb = blocks 1500"
[1] "Num bases in V recomb = blocks 82373"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1035511"
[1] "Numbers of C bases above cutoff is 939599"
[1] "Numbers of V bases above cutoff is 1036507"
[1] "Number of iSNP positions = 5168"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 13"
[1] "R only rare iSNPs (RonlyRIrare) = 1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 13"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 23"
[1] "C only rare iSNPs (ConlyRIrare) = 20"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 1"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 576"
[1] "V only rare iSNPs (VonlyRIrare) = 266"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 74"
[1] "RC only fixed SNPs (RConlyF) = 13"
[1] "RC only rare fixed SNPs (RConlyFrare) = 13"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 726"
[1] "All rare fixed SNPs (AllFrare) = 508"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 332"
[1] "All iSNPs (AllRI) = 11"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 1"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 1"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 416"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 1"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 161 rows containing missing values (geom_point).
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 171 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 318"
[1] "Number cDenovo Non-Ref SNPs for C = 1388"
[1] "Number cDenovo iSNPs for C = 3"
[1] "Number cDenovo Ref SNPs for R = 339"
[1] "Number cDenovo Non-Ref SNPs for R = 1525"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 192"
[1] "Number cDenovo Non-Ref SNPs for V = 102"
[1] "Number cDenovo iSNPs for V = 1572"
[[1]]
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Subject 68
SNP_analysis_pipeline(subject_id = 68)
[1] "SUBJECT_ID is 68"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 66"
[1] "Num bases in R recomb = blocks 206"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1033503"
[1] "Numbers of C bases above cutoff is 1035903"
[1] "Numbers of V bases above cutoff is 1034542"
[1] "Number of iSNP positions = 5247"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 6"
[1] "R only rare iSNPs (RonlyRIrare) = 1"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 4"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 2"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5189"
[1] "All rare fixed SNPs (AllFrare) = 1006"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 11"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 6"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 1"
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 12 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 340"
[1] "Number cDenovo Non-Ref SNPs for C = 1527"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 337"
[1] "Number cDenovo Non-Ref SNPs for R = 1528"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 341"
[1] "Number cDenovo Non-Ref SNPs for V = 1526"
[1] "Number cDenovo iSNPs for V = 2"
[[1]]
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Subject 72
SNP_analysis_pipeline(subject_id = 72)
[1] "SUBJECT_ID is 72"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 73594"
[1] "Num bases in R recomb = blocks 72610"
[1] "Num bases in V recomb = blocks 44984"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 344563"
[1] "Numbers of C bases above cutoff is 1011352"
[1] "Numbers of V bases above cutoff is 1029389"
[1] "Number of iSNP positions = 617"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 49"
[1] "R only rare iSNPs (RonlyRIrare) = 44"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 35"
[1] "V only rare iSNPs (VonlyRIrare) = 22"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 9"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 1"
[1] "All fixed SNPs (AllF) = 512"
[1] "All rare fixed SNPs (AllFrare) = 295"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 104"
[1] "All iSNPs (AllRI) = 1"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 59 rows containing missing values (geom_point).
Warning: Removed 1254 rows containing missing values (geom_point).
Warning: Removed 26 rows containing missing values (geom_point).
Warning: Removed 1339 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1570"
[1] "Number cDenovo Non-Ref SNPs for C = 243"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 542"
[1] "Number cDenovo Non-Ref SNPs for R = 76"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 1600"
[1] "Number cDenovo Non-Ref SNPs for V = 246"
[1] "Number cDenovo iSNPs for V = 0"
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Subject 87
SNP_analysis_pipeline(subject_id = 87)
[1] "SUBJECT_ID is 87"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1016254"
[1] "Numbers of C bases above cutoff is 1035662"
[1] "Numbers of V bases above cutoff is 1025249"
[1] "Number of iSNP positions = 1200"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 77"
[1] "R only rare iSNPs (RonlyRIrare) = 55"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 3"
[1] "C only rare iSNPs (ConlyRIrare) = 3"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 61"
[1] "V only rare iSNPs (VonlyRIrare) = 40"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 3"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 992"
[1] "All rare fixed SNPs (AllFrare) = 690"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 1"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 1"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 4"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 5"
Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 49 rows containing missing values (geom_point).
Warning: Removed 24 rows containing missing values (geom_point).
Warning: Removed 88 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1589"
[1] "Number cDenovo Non-Ref SNPs for C = 268"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 1550"
[1] "Number cDenovo Non-Ref SNPs for R = 257"
[1] "Number cDenovo iSNPs for R = 16"
[1] "Number cDenovo Ref SNPs for V = 1574"
[1] "Number cDenovo Non-Ref SNPs for V = 263"
[1] "Number cDenovo iSNPs for V = 11"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 98
SNP_analysis_pipeline(subject_id = 98)
[1] "SUBJECT_ID is 98"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1038078"
[1] "Numbers of C bases above cutoff is 1004338"
[1] "Numbers of V bases above cutoff is 1035500"
[1] "Number of iSNP positions = 1301"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 27"
[1] "R only rare iSNPs (RonlyRIrare) = 15"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 47"
[1] "V only rare iSNPs (VonlyRIrare) = 39"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 31"
[1] "RV only rare iSNPs (RVonlyRIrare) = 3"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 1159"
[1] "All rare fixed SNPs (AllFrare) = 792"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 3"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 13"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 79 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 87 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1552"
[1] "Number cDenovo Non-Ref SNPs for C = 241"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 1610"
[1] "Number cDenovo Non-Ref SNPs for R = 259"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 1611"
[1] "Number cDenovo Non-Ref SNPs for V = 256"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 107
SNP_analysis_pipeline(subject_id = 107)
[1] "SUBJECT_ID is 107"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 951"
[1] "Num bases in R recomb = blocks 951"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036634"
[1] "Numbers of C bases above cutoff is 792534"
[1] "Numbers of V bases above cutoff is 1029789"
[1] "Number of iSNP positions = 3726"
[1] "R only fixed SNPs (RonlyF) = 2"
[1] "R only rare fixed SNPs (RonlyFrare) = 2"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 34"
[1] "R only rare iSNPs (RonlyRIrare) = 13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 34"
[1] "C only rare iSNPs (ConlyRIrare) = 34"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 65"
[1] "V only rare iSNPs (VonlyRIrare) = 51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 25"
[1] "RV only rare iSNPs (RVonlyRIrare) = 4"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 3546"
[1] "All rare fixed SNPs (AllFrare) = 674"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 32"
[1] "All iSNPs (AllRI) = 0"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 276 rows containing missing values (geom_point).
Warning: Removed 14 rows containing missing values (geom_point).
Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 305 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 291"
[1] "Number cDenovo Non-Ref SNPs for C = 1304"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 337"
[1] "Number cDenovo Non-Ref SNPs for R = 1520"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 338"
[1] "Number cDenovo Non-Ref SNPs for V = 1518"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 192
SNP_analysis_pipeline(subject_id = 192)
[1] "SUBJECT_ID is 192"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 47748"
[1] "Num bases in R recomb = blocks 47523"
[1] "Num bases in V recomb = blocks 47523"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036095"
[1] "Numbers of C bases above cutoff is 1028769"
[1] "Numbers of V bases above cutoff is 1037030"
[1] "Number of iSNP positions = 5297"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 20"
[1] "R only rare iSNPs (RonlyRIrare) = 13"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 1"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 64"
[1] "V only rare iSNPs (VonlyRIrare) = 51"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 3"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 2"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 46"
[1] "RV only rare iSNPs (RVonlyRIrare) = 7"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5115"
[1] "All rare fixed SNPs (AllFrare) = 1215"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 81"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 2"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 4"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 1"
Warning: Removed 18 rows containing missing values (geom_point).
Warning: Removed 10 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 30 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 317"
[1] "Number cDenovo Non-Ref SNPs for C = 1534"
[1] "Number cDenovo iSNPs for C = 1"
[1] "Number cDenovo Ref SNPs for R = 321"
[1] "Number cDenovo Non-Ref SNPs for R = 1539"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 323"
[1] "Number cDenovo Non-Ref SNPs for V = 1545"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 227
SNP_analysis_pipeline(subject_id = 227)
[1] "SUBJECT_ID is 227"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 16439"
[1] "Num bases in R recomb = blocks 14887"
[1] "Num bases in V recomb = blocks 14887"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 822591"
[1] "Numbers of C bases above cutoff is 1034715"
[1] "Numbers of V bases above cutoff is 1038235"
[1] "Number of iSNP positions = 999"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 178"
[1] "R only rare iSNPs (RonlyRIrare) = 149"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 6"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 3"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 798"
[1] "All rare fixed SNPs (AllFrare) = 540"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 27"
[1] "All iSNPs (AllRI) = 4"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 427 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 442 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1623"
[1] "Number cDenovo Non-Ref SNPs for C = 237"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 1257"
[1] "Number cDenovo Non-Ref SNPs for R = 179"
[1] "Number cDenovo iSNPs for R = 9"
[1] "Number cDenovo Ref SNPs for V = 1630"
[1] "Number cDenovo Non-Ref SNPs for V = 239"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 362
SNP_analysis_pipeline(subject_id = 362)
[1] "SUBJECT_ID is 362"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 168863"
[1] "Num bases in R recomb = blocks 168863"
[1] "Num bases in V recomb = blocks 168755"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1031572"
[1] "Numbers of C bases above cutoff is 1032552"
[1] "Numbers of V bases above cutoff is 1038383"
[1] "Number of iSNP positions = 2002"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 10"
[1] "R only rare iSNPs (RonlyRIrare) = 9"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 1"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 3"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 5"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 1944"
[1] "All rare fixed SNPs (AllFrare) = 879"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 809"
[1] "All iSNPs (AllRI) = 13"
[1] "All rare iSNPs (AllRIrare) = 1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 2"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 2"
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 24 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 32 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1627"
[1] "Number cDenovo Non-Ref SNPs for C = 239"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 1611"
[1] "Number cDenovo Non-Ref SNPs for R = 236"
[1] "Number cDenovo iSNPs for R = 1"
[1] "Number cDenovo Ref SNPs for V = 1630"
[1] "Number cDenovo Non-Ref SNPs for V = 240"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 519
SNP_analysis_pipeline(subject_id = 519)
[1] "SUBJECT_ID is 519"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 395"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 226"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 818552"
[1] "Numbers of C bases above cutoff is 1020321"
[1] "Numbers of V bases above cutoff is 1034717"
[1] "Number of iSNP positions = 3957"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 27"
[1] "R only rare iSNPs (RonlyRIrare) = 27"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 3"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 3913"
[1] "All rare fixed SNPs (AllFrare) = 780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 16"
[1] "All iSNPs (AllRI) = 4"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 38 rows containing missing values (geom_point).
Warning: Removed 384 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 427 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 334"
[1] "Number cDenovo Non-Ref SNPs for C = 1498"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 283"
[1] "Number cDenovo Non-Ref SNPs for R = 1202"
[1] "Number cDenovo iSNPs for R = 1"
[1] "Number cDenovo Ref SNPs for V = 342"
[1] "Number cDenovo Non-Ref SNPs for V = 1523"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 564
SNP_analysis_pipeline(subject_id = 564)
[1] "SUBJECT_ID is 564"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 23231"
[1] "Num bases in V recomb = blocks 23231"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1035161"
[1] "Numbers of C bases above cutoff is 1030082"
[1] "Numbers of V bases above cutoff is 1013781"
[1] "Number of iSNP positions = 5253"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 0"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 231"
[1] "C only rare fixed SNPs (ConlyFrare) = 57"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 101"
[1] "C only iSNPs (ConlyRI) = 4"
[1] "C only rare iSNPs (ConlyRIrare) = 4"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 58"
[1] "V only rare iSNPs (VonlyRIrare) = 53"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 179"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 96"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 58"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 4668"
[1] "All rare fixed SNPs (AllFrare) = 881"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 20"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 1"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 20 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 39 rows containing missing values (geom_point).
Warning: Removed 61 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 338"
[1] "Number cDenovo Non-Ref SNPs for C = 1513"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 344"
[1] "Number cDenovo Non-Ref SNPs for R = 1524"
[1] "Number cDenovo iSNPs for R = 1"
[1] "Number cDenovo Ref SNPs for V = 332"
[1] "Number cDenovo Non-Ref SNPs for V = 1475"
[1] "Number cDenovo iSNPs for V = 25"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 753
SNP_analysis_pipeline(subject_id = 753)
[1] "SUBJECT_ID is 753"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 619998"
[1] "Numbers of C bases above cutoff is 1037605"
[1] "Numbers of V bases above cutoff is 1037470"
[1] "Number of iSNP positions = 912"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 233"
[1] "R only rare iSNPs (RonlyRIrare) = 105"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 623"
[1] "All rare fixed SNPs (AllFrare) = 426"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 2"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 9"
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 771 rows containing missing values (geom_point).
Warning: Removed 6 rows containing missing values (geom_point).
Warning: Removed 781 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1609"
[1] "Number cDenovo Non-Ref SNPs for C = 259"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 926"
[1] "Number cDenovo Non-Ref SNPs for R = 143"
[1] "Number cDenovo iSNPs for R = 32"
[1] "Number cDenovo Ref SNPs for V = 1608"
[1] "Number cDenovo Non-Ref SNPs for V = 258"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 908
SNP_analysis_pipeline(subject_id = 908)
[1] "SUBJECT_ID is 908"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 1485"
[1] "Num bases in R recomb = blocks 1691"
[1] "Num bases in V recomb = blocks 1485"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1033470"
[1] "Numbers of C bases above cutoff is 1032274"
[1] "Numbers of V bases above cutoff is 1006412"
[1] "Number of iSNP positions = 5112"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 0"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 15"
[1] "C only rare iSNPs (ConlyRIrare) = 6"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 86"
[1] "V only rare iSNPs (VonlyRIrare) = 80"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 4852"
[1] "All rare fixed SNPs (AllFrare) = 928"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 35"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 5"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 65 rows containing missing values (geom_point).
Warning: Removed 78 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 340"
[1] "Number cDenovo Non-Ref SNPs for C = 1526"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 340"
[1] "Number cDenovo Non-Ref SNPs for R = 1523"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 329"
[1] "Number cDenovo Non-Ref SNPs for V = 1450"
[1] "Number cDenovo iSNPs for V = 27"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 927
SNP_analysis_pipeline(subject_id = 927)
[1] "SUBJECT_ID is 927"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 27215"
[1] "Num bases in R recomb = blocks 27215"
[1] "Num bases in V recomb = blocks 8664"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1026496"
[1] "Numbers of C bases above cutoff is 1034845"
[1] "Numbers of V bases above cutoff is 1034464"
[1] "Number of iSNP positions = 5283"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 2"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 4"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 1"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5244"
[1] "All rare fixed SNPs (AllFrare) = 1247"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 142"
[1] "All iSNPs (AllRI) = 24"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 1"
Warning: Removed 11 rows containing missing values (geom_point).
Warning: Removed 25 rows containing missing values (geom_point).
Warning: Removed 12 rows containing missing values (geom_point).
Warning: Removed 48 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 328"
[1] "Number cDenovo Non-Ref SNPs for C = 1529"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 323"
[1] "Number cDenovo Non-Ref SNPs for R = 1520"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 326"
[1] "Number cDenovo Non-Ref SNPs for V = 1530"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 951
SNP_analysis_pipeline(subject_id = 951)
[1] "SUBJECT_ID is 951"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 13256"
[1] "Num bases in R recomb = blocks 16904"
[1] "Num bases in V recomb = blocks 13256"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1013234"
[1] "Numbers of C bases above cutoff is 1035195"
[1] "Numbers of V bases above cutoff is 1035300"
[1] "Number of iSNP positions = 5191"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 14"
[1] "R only rare iSNPs (RonlyRIrare) = 2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 8"
[1] "V only rare iSNPs (VonlyRIrare) = 1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 2"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5069"
[1] "All rare fixed SNPs (AllFrare) = 1083"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 84"
[1] "All iSNPs (AllRI) = 17"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 4"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 18"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 63 rows containing missing values (geom_point).
Warning: Removed 9 rows containing missing values (geom_point).
Warning: Removed 76 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 334"
[1] "Number cDenovo Non-Ref SNPs for C = 1533"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 323"
[1] "Number cDenovo Non-Ref SNPs for R = 1485"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 333"
[1] "Number cDenovo Non-Ref SNPs for V = 1528"
[1] "Number cDenovo iSNPs for V = 1"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 968
SNP_analysis_pipeline(subject_id = 968)
[1] "SUBJECT_ID is 968"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 0"
[1] "Num bases in V recomb = blocks 0"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 578500"
[1] "Numbers of C bases above cutoff is 1029349"
[1] "Numbers of V bases above cutoff is 1037840"
[1] "Number of iSNP positions = 1245"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 537"
[1] "R only rare iSNPs (RonlyRIrare) = 114"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 586"
[1] "All rare fixed SNPs (AllFrare) = 403"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 0"
[1] "All iSNPs (AllRI) = 9"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 19"
Warning: Removed 20 rows containing missing values (geom_point).
Warning: Removed 984 rows containing missing values (geom_point).
Warning: Removed 2 rows containing missing values (geom_point).
Warning: Removed 1006 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1607"
[1] "Number cDenovo Non-Ref SNPs for C = 244"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 671"
[1] "Number cDenovo Non-Ref SNPs for R = 84"
[1] "Number cDenovo iSNPs for R = 132"
[1] "Number cDenovo Ref SNPs for V = 1623"
[1] "Number cDenovo Non-Ref SNPs for V = 246"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1077
SNP_analysis_pipeline(subject_id = 1077)
[1] "SUBJECT_ID is 1077"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 15083"
[1] "Num bases in R recomb = blocks 14177"
[1] "Num bases in V recomb = blocks 14758"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 798730"
[1] "Numbers of C bases above cutoff is 1036188"
[1] "Numbers of V bases above cutoff is 979111"
[1] "Number of iSNP positions = 3956"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 154"
[1] "R only rare iSNPs (RonlyRIrare) = 109"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 4"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 59"
[1] "V only rare iSNPs (VonlyRIrare) = 47"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 3145"
[1] "All rare fixed SNPs (AllFrare) = 620"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 132"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 2"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 26"
Warning: Removed 5 rows containing missing values (geom_point).
Warning: Removed 440 rows containing missing values (geom_point).
Warning: Removed 109 rows containing missing values (geom_point).
Warning: Removed 554 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 338"
[1] "Number cDenovo Non-Ref SNPs for C = 1528"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 249"
[1] "Number cDenovo Non-Ref SNPs for R = 1053"
[1] "Number cDenovo iSNPs for R = 129"
[1] "Number cDenovo Ref SNPs for V = 315"
[1] "Number cDenovo Non-Ref SNPs for V = 1432"
[1] "Number cDenovo iSNPs for V = 15"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1078
SNP_analysis_pipeline(subject_id = 1078)
[1] "SUBJECT_ID is 1078"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 0"
[1] "Num bases in R recomb = blocks 22555"
[1] "Num bases in V recomb = blocks 35303"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 875018"
[1] "Numbers of C bases above cutoff is 249618"
[1] "Numbers of V bases above cutoff is 1015869"
[1] "Number of iSNP positions = 1382"
[1] "R only fixed SNPs (RonlyF) = 96"
[1] "R only rare fixed SNPs (RonlyFrare) = 40"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 9"
[1] "R only iSNPs (RonlyRI) = 103"
[1] "R only rare iSNPs (RonlyRIrare) = 65"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 20"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 85"
[1] "C only rare iSNPs (ConlyRIrare) = 74"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 6"
[1] "V only fixed SNPs (VonlyF) = 1"
[1] "V only rare fixed SNPs (VonlyFrare) = 1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 35"
[1] "V only rare iSNPs (VonlyRIrare) = 34"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 1"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 33"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 3"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 91"
[1] "RV only rare iSNPs (RVonlyRIrare) = 5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 25"
[1] "VC only fixed SNPs (VConlyF) = 4"
[1] "VC only rare fixed SNPs (VConlyFrare) = 2"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 1"
[1] "VC only iSNPs (VConlyRI) = 17"
[1] "VC only rare iSNPs (VConlyRIrare) = 10"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 4"
[1] "All fixed SNPs (AllF) = 32"
[1] "All rare fixed SNPs (AllFrare) = 32"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 8"
[1] "All iSNPs (AllRI) = 65"
[1] "All rare iSNPs (AllRIrare) = 1"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 2"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 51"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 54"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 58"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 8"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 5"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 58"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 58"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 1332 rows containing missing values (geom_point).
Warning: Removed 256 rows containing missing values (geom_point).
Warning: Removed 23 rows containing missing values (geom_point).
Warning: Removed 1611 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 279"
[1] "Number cDenovo Non-Ref SNPs for C = 21"
[1] "Number cDenovo iSNPs for C = 234"
[1] "Number cDenovo Ref SNPs for R = 265"
[1] "Number cDenovo Non-Ref SNPs for R = 1164"
[1] "Number cDenovo iSNPs for R = 181"
[1] "Number cDenovo Ref SNPs for V = 624"
[1] "Number cDenovo Non-Ref SNPs for V = 80"
[1] "Number cDenovo iSNPs for V = 1139"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1079
SNP_analysis_pipeline(subject_id = 1079)
[1] "SUBJECT_ID is 1079"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 25694"
[1] "Num bases in R recomb = blocks 19690"
[1] "Num bases in V recomb = blocks 12657"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1018215"
[1] "Numbers of C bases above cutoff is 1036824"
[1] "Numbers of V bases above cutoff is 1035527"
[1] "Number of iSNP positions = 5450"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 299"
[1] "R only rare iSNPs (RonlyRIrare) = 137"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 5"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 22"
[1] "V only rare iSNPs (VonlyRIrare) = 8"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 1"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 19"
[1] "RV only rare iSNPs (RVonlyRIrare) = 1"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 2169"
[1] "All rare fixed SNPs (AllFrare) = 858"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 197"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 10"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 13"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 132"
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 46 rows containing missing values (geom_point).
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 53 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 336"
[1] "Number cDenovo Non-Ref SNPs for C = 1532"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 244"
[1] "Number cDenovo Non-Ref SNPs for R = 714"
[1] "Number cDenovo iSNPs for R = 867"
[1] "Number cDenovo Ref SNPs for V = 322"
[1] "Number cDenovo Non-Ref SNPs for V = 1393"
[1] "Number cDenovo iSNPs for V = 152"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1106
SNP_analysis_pipeline(subject_id = 1106)
[1] "SUBJECT_ID is 1106"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 26943"
[1] "Num bases in R recomb = blocks 26722"
[1] "Num bases in V recomb = blocks 3510"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1024517"
[1] "Numbers of C bases above cutoff is 1032626"
[1] "Numbers of V bases above cutoff is 1038242"
[1] "Number of iSNP positions = 692"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 0"
[1] "R only rare iSNPs (RonlyRIrare) = 0"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 1"
[1] "V only rare iSNPs (VonlyRIrare) = 1"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 1"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 1"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 1"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 667"
[1] "All rare fixed SNPs (AllFrare) = 425"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 137"
[1] "All iSNPs (AllRI) = 6"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 1"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 7"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 21 rows containing missing values (geom_point).
Warning: Removed 42 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 70 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1701"
[1] "Number cDenovo Non-Ref SNPs for C = 149"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 1682"
[1] "Number cDenovo Non-Ref SNPs for R = 147"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 1711"
[1] "Number cDenovo Non-Ref SNPs for V = 153"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1145
SNP_analysis_pipeline(subject_id = 1145)
[1] "SUBJECT_ID is 1145"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 497"
[1] "Num bases in R recomb = blocks 261"
[1] "Num bases in V recomb = blocks 177"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1026277"
[1] "Numbers of C bases above cutoff is 1034922"
[1] "Numbers of V bases above cutoff is 888302"
[1] "Number of iSNP positions = 4468"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 3"
[1] "R only rare iSNPs (RonlyRIrare) = 2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 1"
[1] "C only rare iSNPs (ConlyRIrare) = 1"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 139"
[1] "V only rare iSNPs (VonlyRIrare) = 116"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 2"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 1"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 4155"
[1] "All rare fixed SNPs (AllFrare) = 780"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 20"
[1] "All iSNPs (AllRI) = 7"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 8"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 29 rows containing missing values (geom_point).
Warning: Removed 284 rows containing missing values (geom_point).
Warning: Removed 317 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 336"
[1] "Number cDenovo Non-Ref SNPs for C = 1529"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 328"
[1] "Number cDenovo Non-Ref SNPs for R = 1512"
[1] "Number cDenovo iSNPs for R = 0"
[1] "Number cDenovo Ref SNPs for V = 281"
[1] "Number cDenovo Non-Ref SNPs for V = 1265"
[1] "Number cDenovo iSNPs for V = 39"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1176
SNP_analysis_pipeline(subject_id = 1176)
[1] "SUBJECT_ID is 1176"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 51945"
[1] "Num bases in R recomb = blocks 14626"
[1] "Num bases in V recomb = blocks 13428"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1038149"
[1] "Numbers of C bases above cutoff is 1035843"
[1] "Numbers of V bases above cutoff is 1027021"
[1] "Number of iSNP positions = 6142"
[1] "R only fixed SNPs (RonlyF) = 0"
[1] "R only rare fixed SNPs (RonlyFrare) = 0"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 62"
[1] "R only rare iSNPs (RonlyRIrare) = 29"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 42"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 6"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 1"
[1] "V only fixed SNPs (VonlyF) = 1"
[1] "V only rare fixed SNPs (VonlyFrare) = 1"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 528"
[1] "V only rare iSNPs (VonlyRIrare) = 303"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 54"
[1] "RC only fixed SNPs (RConlyF) = 53"
[1] "RC only rare fixed SNPs (RConlyFrare) = 25"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 330"
[1] "RC only rare iSNPs (RConlyRIrare) = 90"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 195"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 18"
[1] "RV only rare iSNPs (RVonlyRIrare) = 5"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 8"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 0"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 380"
[1] "All rare fixed SNPs (AllFrare) = 372"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 47"
[1] "All iSNPs (AllRI) = 322"
[1] "All rare iSNPs (AllRIrare) = 88"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 86"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 7"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 7"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 41"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 504"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 59"
Warning: Removed 4 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 21 rows containing missing values (geom_point).
Warning: Removed 26 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 335"
[1] "Number cDenovo Non-Ref SNPs for C = 1517"
[1] "Number cDenovo iSNPs for C = 16"
[1] "Number cDenovo Ref SNPs for R = 333"
[1] "Number cDenovo Non-Ref SNPs for R = 1373"
[1] "Number cDenovo iSNPs for R = 165"
[1] "Number cDenovo Ref SNPs for V = 189"
[1] "Number cDenovo Non-Ref SNPs for V = 94"
[1] "Number cDenovo iSNPs for V = 1568"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1182
SNP_analysis_pipeline(subject_id = 1182)
[1] "SUBJECT_ID is 1182"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 1474"
[1] "Num bases in R recomb = blocks 3396"
[1] "Num bases in V recomb = blocks 24510"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1036038"
[1] "Numbers of C bases above cutoff is 1029053"
[1] "Numbers of V bases above cutoff is 1035249"
[1] "Number of iSNP positions = 5725"
[1] "R only fixed SNPs (RonlyF) = 20"
[1] "R only rare fixed SNPs (RonlyFrare) = 13"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 361"
[1] "R only rare iSNPs (RonlyRIrare) = 165"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 33"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 10"
[1] "C only rare iSNPs (ConlyRIrare) = 7"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 1"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 2"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 19"
[1] "RV only rare iSNPs (RVonlyRIrare) = 8"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 3"
[1] "VC only fixed SNPs (VConlyF) = 470"
[1] "VC only rare fixed SNPs (VConlyFrare) = 207"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 36"
[1] "VC only iSNPs (VConlyRI) = 27"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 10"
[1] "All fixed SNPs (AllF) = 241"
[1] "All rare fixed SNPs (AllFrare) = 218"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 50"
[1] "All iSNPs (AllRI) = 3"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 91"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 31"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 508"
Warning: Removed 29 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 46 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 334"
[1] "Number cDenovo Non-Ref SNPs for C = 1509"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 370"
[1] "Number cDenovo Non-Ref SNPs for R = 59"
[1] "Number cDenovo iSNPs for R = 1442"
[1] "Number cDenovo Ref SNPs for V = 331"
[1] "Number cDenovo Non-Ref SNPs for V = 1358"
[1] "Number cDenovo iSNPs for V = 167"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1201
SNP_analysis_pipeline(subject_id = 1201)
[1] "SUBJECT_ID is 1201"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 803"
[1] "Num bases in R recomb = blocks 184"
[1] "Num bases in V recomb = blocks 670"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1038120"
[1] "Numbers of C bases above cutoff is 1025145"
[1] "Numbers of V bases above cutoff is 1037114"
[1] "Number of iSNP positions = 1147"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 11"
[1] "R only rare iSNPs (RonlyRIrare) = 2"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 0"
[1] "C only rare iSNPs (ConlyRIrare) = 0"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 0"
[1] "V only rare iSNPs (VonlyRIrare) = 0"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 2"
[1] "VC only rare iSNPs (VConlyRIrare) = 1"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 1086"
[1] "All rare fixed SNPs (AllFrare) = 729"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 14"
[1] "All iSNPs (AllRI) = 10"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 18"
Warning: Removed 36 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_point).
Warning: Removed 7 rows containing missing values (geom_point).
Warning: Removed 44 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 1597"
[1] "Number cDenovo Non-Ref SNPs for C = 237"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 1621"
[1] "Number cDenovo Non-Ref SNPs for R = 246"
[1] "Number cDenovo iSNPs for R = 2"
[1] "Number cDenovo Ref SNPs for V = 1617"
[1] "Number cDenovo Non-Ref SNPs for V = 246"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









Subject 1226
SNP_analysis_pipeline(subject_id = 1226)
[1] "SUBJECT_ID is 1226"
[1] "Rare iSNP cutoff = 3"
[1] "num rare iSNPs = 4383"
[1] "num common iSNPs = 4970"
[1] "Recombination block cutoff = 3"
[1] "Num bases in C recomb blocks= 4431"
[1] "Num bases in R recomb = blocks 4431"
[1] "Num bases in V recomb = blocks 4431"
[1] "Coverage cutoff = 10"
[1] "Numbers of R bases above cutoff is 1018587"
[1] "Numbers of C bases above cutoff is 1035547"
[1] "Numbers of V bases above cutoff is 1033213"
[1] "Number of iSNP positions = 5206"
[1] "R only fixed SNPs (RonlyF) = 1"
[1] "R only rare fixed SNPs (RonlyFrare) = 1"
[1] "R only fixed SNPs in recombinant regions (RonlyFrecomb) = 0"
[1] "R only iSNPs (RonlyRI) = 26"
[1] "R only rare iSNPs (RonlyRIrare) = 22"
[1] "R only iSNPs in recombinant regions (RonlyRIrecomb) = 0"
[1] "C only fixed SNPs (ConlyF) = 0"
[1] "C only rare fixed SNPs (ConlyFrare) = 0"
[1] "C only fixed SNPs in recombinant regions (ConlyFrecomb) = 0"
[1] "C only iSNPs (ConlyRI) = 2"
[1] "C only rare iSNPs (ConlyRIrare) = 2"
[1] "C only iSNPs in recombinant regions (ConlyRIrecomb) = 0"
[1] "V only fixed SNPs (VonlyF) = 0"
[1] "V only rare fixed SNPs (VonlyFrare) = 0"
[1] "V only fixed SNPs in recombinant regions (VonlyFrecombb) = 0"
[1] "V only iSNPs (VonlyRI) = 2"
[1] "V only rare iSNPs (VonlyRIrare) = 2"
[1] "V only iSNPs in recombinant regions (VonlyRIrecomb) = 0"
[1] "RC only fixed SNPs (RConlyF) = 0"
[1] "RC only rare fixed SNPs (RConlyFrare) = 0"
[1] "RC only fixed SNPs in recombinant regions (RConlyFrecomb) = 0"
[1] "RC only iSNPs (RConlyRI) = 0"
[1] "RC only rare iSNPs (RConlyRIrare) = 0"
[1] "RC only iSNPs in recombinant regions (RConlyRIrecomb) = 0"
[1] "RV only fixed SNPs (RVonlyF) = 0"
[1] "RV only rare fixed SNPs (RVonlyFrare) = 0"
[1] "RV only fixed SNPs in recombinant regions (RVonlyFrecomb) = 0"
[1] "RV only iSNPs (RVonlyRI) = 0"
[1] "RV only rare iSNPs (RVonlyRIrare) = 0"
[1] "RV only iSNPs in recombinant regions (RVonlyRIrecomb) = 0"
[1] "VC only fixed SNPs (VConlyF) = 0"
[1] "VC only rare fixed SNPs (VConlyFrare) = 0"
[1] "VC only fixed SNPs in recombinant regions (VConlyFrecomb) = 0"
[1] "VC only iSNPs (VConlyRI) = 1"
[1] "VC only rare iSNPs (VConlyRIrare) = 0"
[1] "VC only iSNPs in recombinant regions (VConlyRIrecomb) = 0"
[1] "All fixed SNPs (AllF) = 5134"
[1] "All rare fixed SNPs (AllFrare) = 1056"
[1] "All fixed SNPs in recombinant regions (AllFrecomb) = 1"
[1] "All iSNPs (AllRI) = 24"
[1] "All rare iSNPs (AllRIrare) = 0"
[1] "All iSNPs in recombinant regions (AllRIrecomb) = 0"
[1] "R is fixed, V only is intermediate, and rare (RonlyF_VIrare) = 0"
[1] "R is fixed, C only is intermediate, and rare (RonlyF_CIrare) = 0"
[1] "R is fixed, V and C are intermediate, and rare (RonlyF_CandVIrare) = 0"
[1] "C is fixed, V only is intermediate, and rare (ConlyF_VIrare) = 0"
[1] "C is fixed, R only is intermediate, and rare (ConlyF_RIrare) = 0"
[1] "C is fixed, R and V are intermediate, and rare (ConlyF_RandVIrare) = 0"
[1] "V is fixed, C only is intermediate, and rare (VonlyF_CIrare) = 0"
[1] "V is fixed, R only is intermediate, and rare (VonlyF_RIrare) = 0"
[1] "V is fixed, R and C are intermediate, and rare (VonlyF_CandRIrare) = 0"
[1] "R and C are fixed, V is intermediate, and rare (RCF_VIrare) = 0"
[1] "R and V are fixed, C is intermediate, and rare (RVF_CIrare) = 0"
[1] "V and C are fixed, R is intermediate, and rare (CVF_RIrare) = 0"
Warning: Removed 3 rows containing missing values (geom_point).
Warning: Removed 15 rows containing missing values (geom_point).
Warning: Removed 10 rows containing missing values (geom_point).
Warning: Removed 28 rows containing non-finite values (stat_boxplot).
[1] "Number cDenovo Ref SNPs for C = 342"
[1] "Number cDenovo Non-Ref SNPs for C = 1526"
[1] "Number cDenovo iSNPs for C = 0"
[1] "Number cDenovo Ref SNPs for R = 337"
[1] "Number cDenovo Non-Ref SNPs for R = 1517"
[1] "Number cDenovo iSNPs for R = 2"
[1] "Number cDenovo Ref SNPs for V = 337"
[1] "Number cDenovo Non-Ref SNPs for V = 1524"
[1] "Number cDenovo iSNPs for V = 0"
[[1]]
[[2]]
[[3]]
[[4]]
[[5]]
[[6]]
[[7]]
[[8]]
[[9]]









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